Evolution of the genomes of two nematodes in the ... - Ken Wolfe

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A B b1 b2 C. briggsae chromosome A T T e1 e2
Breakpoint type Number of Breakpoints P-value Translocation 445 3.3×10 −5 Inversion 185 0.10 Transposition 469 2.9×10 −4 The number of rearrangement breakpoints in intergenic spacers containing at least one of 33 dispersed repeat families was compared with the number of intergenic spacers in the genome containing one or more dispersed repeats. Only intergenic spacers of 10 kb or shorter were included, of which there are 16,574 in the Caenorhabditis elegans genome. The P-values for one-sided χ 2 tests are given after applying the Bonferroni correction for multiple testing (multiplies the raw P-values by 3). Table 2.1: Association of Rearrangement Breakpoints with Repeats. there have been ∼10,200 chromosome breakages since speciation, which is 5100 breakages per species, or ∼51 breakages/Mb. Using our 50–120-Mya divergence date, this implies a rate of 42–102 breakages/Myr, or 0.4–1.0 breakages/Mb per Myr. 2.2.6 Association of Breakpoints with Repetitive DNA We obtained the distribution of 33 dispersed repeat sequences in the C. elegans genome from WormBase (http://www.sanger.ac.uk/Projects/C elegans/WORMBASE/GFF files.shtml; Stein et al., 2001). When we pool all 33 repeats, there is a significant association between dispersed repeats and both translocation and transposition breakpoints in C. elegans (Table 2.1). However, no association is seen for inversion breakpoints. For two individual dispersed repeats, the association with transposition breakpoints is significant (P < 0.05; Table 2.2): CeRep20 and CeRep37. However, the significance of the association is marginal for CeRep20 (P = 0.045), whereas the small sample size for CeRep37 makes the test result unreliable. Translocation breakpoints tend to be next to four different repeats: CeRep13, CeRep15, CeRep19, and CeRep32. C. elegans has compound repeats, listed on the Sanger Institute web site (http://www.sanger. ac.uk/Projects/C elegans/repeats/). The only one associated with translocation breakpoints is CeRep13-CeRep18-CeRep18-CeRep33-CeRep18-CeRep13 (P = 0.01; Table 2.2). However, this is simply owing to the association of CeRep13 with breakpoints, because breakpoints are often near CeRep13/CeRep- 18/CeRep33, but not CeRep13 + CeRep18 + CeRep33. The association of CeRep19 and CeRep32 with translocation breakpoints is marginally significant (P ≤ 0.05), but that of CeRep13 and CeRep15 is strong (P ≤ 0.005). CeRep13 is a 26-bp sequence that is repeated ∼1350 times in the C. elegans genome, whereas CeRep15 is a 63-bp sequence of which there are about 910 copies. Both these repeats seem to be derived from transposable elements. CeRep13 is 96% identical over 24 bp to the 24-bp terminal inverted repeat (TIR) of Cele11, which is thought to be a nonautonomous relative of Tc2, a Tc1/mariner family 17
Page 1 and 2: Evolution of the genomes of two nem
Page 3 and 4: Acknowledgements Thankyou a billion
Page 5 and 6: Table of Contents List of Abbreviat
Page 7 and 8: 4.2.3 Phases of Novel Introns . . .
Page 9 and 10: List of Figures 1.1 The model organ
Page 11 and 12: Chapter 1 Overview The biology of t
Page 13 and 14: E Chordates Hemichordates Echinoder
Page 15 and 16: 1.4 TWO Caenorhabditis GENOMES In 2
Page 17 and 18: Chapter 2 Faster Rate of Genome Rea
Page 19 and 20: Nematode fossils are extremely scar
Page 21 and 22: ends) are distributed at random alo
Page 23 and 24: Figure 2.3: (A) Location of conserv
Page 25: Frequency Frequency 60 50 40 30 20
Page 29 and 30: transposon (Oosumi et al., 1996). C
Page 31 and 32: effects compared with the recombina
Page 33 and 34: smaller effective population size t
Page 35 and 36: genes whose chromosomal coordinates
Page 37 and 38: did not group together and/or the D
Page 39 and 40: Chapter 3 The Caenorhabditis briggs
Page 41 and 42: predictions, we chose the predictio
Page 43 and 44: C. briggsae C. elegans WS77 ∗ C.
Page 45 and 46: WS77 WS103 New genes 1275 985 New e
Page 47 and 48: C. elegans chrom. III, 9.8-9.9 Mb *
Page 49 and 50: 4. Each exon-cluster X consisted of
Page 51 and 52: 3.5.4 Estimating the C. briggsae-C.
Page 53 and 54: Chapter 4 Origins of Novel Introns
Page 55 and 56: http://wolfe.gen.tcd.ie/avril/intro
Page 57 and 58: Of the 78 genes that have gained in
Page 59 and 60: novel introns that are either C. el
Page 61 and 62: as supporting this hypothesis are b
Page 63 and 64: 4.4 METHODS 4.4.1 Sources of Sequen
Page 65 and 66: 1. the outgroup for the tree was a
Page 67 and 68: Bibliography Aguinaldo, A. M., J. M
Page 69 and 70: Fedorov, A., X. Cao, S. Saxonov, S.
Page 71 and 72: Logsdon, J. M. J., M. G. Tyshenko,
Page 73 and 74: Sankoff, D. (1999). Comparative map

Evolution of the genomes of two nematodes in the ... - Ken Wolfe

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